RNA interference, or post-transcriptional gene silencing, is common to a diverse set of eukaryotes. It is thought that RNAi defends against the invasion of RNA viruses by specifically targeting double-stranded RNA molecules for degradation. RNAi is also speculated to function in the regulation of gene expression and mobilization of transposable elements, but substantive evidence for these roles has not been obtained. This proposal is specifically intended to address the question of whether RNAi serves as a regulator of the expression of endogenous genes, a function implied by the phenotypes of Arabidopsis lines with mutations in genes involved in the mechanism of RNAi. Genes that are differentially expressed in wild-type and mutant backgrounds of Arabidopsis will be identified by hybridization of RNA populations to Affymetrix microarrays and bioinformatic analyses, and the altered expression of candidate genes will be verified by real-time RT-PCR. The function of genes identified by this approach will be examined by analyzing their mutant phenotypes, using an existing collection of transposon-based enhancer and gene trap lines, and by assessing RNA metabolism in wild type and mutant backgrounds. These experiments should yield fundamental insights into how RNAi influences the regulation of gene expression and genome stability, key issues in genome evolution and disease pathogenesis.